About

Professor Rupa Sridharan holds a Ph.D. from the University of California, Los Angeles, and completed postdoctoral research at the Eli and Edythe Broad Stem Cell Institute at UCLA. She leads the Sridharan Lab, which focuses on the epigenetic control of cell identity. The lab investigates mechanisms underlying cell identity and reprogramming, including the role of histone modifications and chromatin regulators in these processes. Professor Sridharan's research has contributed to understanding how epigenetic factors such as histone methylases and demethylases influence transcriptional regulation and pluripotency acquisition. Her lab has made discoveries related to the prevention of hypertranscription and hyperacetylation by the H3K79 methylase DOT1L, the coordination of histone and DNA demethylation during pluripotency acquisition, and the modulation of transcription elongation by heterochromatin protein 1 family members. The Sridharan Lab is actively engaged in training postdoctoral scholars, graduate students, and undergraduate researchers, advancing knowledge in cellular and molecular mechanisms that govern cell fate and identity.

Research topics

• Biology
• Cell biology
• Endocrinology
• Genetics
• Cancer research
• Immunology

Selected publications

• dCas9-metabolic enzyme fusions modulate global and locus-specific gene expression

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-05-10

  articleOpen access

  Abstract Central metabolites function as essential co-substrates for chromatin-modifying enzymes, directly linking cellular metabolism to chromatin regulation. Accordingly, whole-cell fluctuations in co-substrate availabilities have been shown to promote diverse phenotypes through chromatin-dependent mechanisms. There is emerging evidence that metabolic enzymes producing co-substrates for chromatin modifying enzymes can exist in the nucleus, suggesting that nucleus-specific metabolite availability regulates chromatin state. Here, we developed CRISPRm (CRISPR metabolite) to assess how nucleus-specific metabolic perturbations influence chromatin function. Five dCas9-metabolic enzyme fusions ( i.e ., dCas9-ACSS2, -NMNAT1, -MAT2A, -GDH, and -AHCY) were used to modulate nuclear levels of essential co-substrates involved in histone (de)acetylation and (de)methylation reactions. Transient expression of all dCas9 fusions in HEK293T cells induced distinct global changes in gene expression patterns, with dCas9-ACSS2 (acetyl-CoA producing) and NMNAT1 (NAD + producing) eliciting large opposing changes in gene expression, suggesting transcriptional responses to nuclear acetyl-CoA and NAD + production may be directly facilitated by acetylation or deacetylation reactions, respectively. Targeting dCas9-ACSS2 and -NMNAT1 to promoters of select candidate genes revealed enhanced transcriptional modulation. dCas9-ACSS2 upregulated, and dCas9-NMNAT1 downregulated genes showed basal enrichment of H3K9ac, H3K18ac, H3K27ac, H3K4me3, and p300, suggesting these genomic loci reside within epigenetic environments susceptible to fluctuations in acetyl-CoA and NAD + availability. Of significant genes altered, dCas9-MAT2A (SAM producing) increased expression of 72% whereas dCAS9-GDH (alpha-ketoglutarate producing) decreased expression of 79%. Surprisingly, dCAS9-AHCY (SAH hydrolysis) led to down-regulation of shared genes up-regulated by dCas9-MAT2A. The observations amongst the methylation-specific enzymes revealed unexpected and unique gene-regulatory sensitivities to SAM, SAH and alpha-ketoglutarate. Together, these results demonstrate the utility of CRISPRm in studying nuclear metabolic regulation of transcription and provide strong evidence that perturbations in nuclear co-substrates do not lead to a large mass- action changes in chromatin acetylation/methylation but rather to modulation of select chromatin-modifying enzymes with targeted transcription responses. Highlights CRISPRm is a novel, modular dCas9-effector platform that enables interrogation of the metabolism-epigenome axis dCas9-ACSS2, -NMNAT1, -MAT2A, -AHCY, and -GDH induce distinct transcriptional programs. Targeting CRISPRm to promoters enhances transcriptional responses. dCas9-ACSS2 and -NMNAT1 sensitive gene promoters exhibit unique enrichment of chromatin features, including H3K9ac, H3K18ac, H3K27ac, H3K4me3 and p300.

  PublisherDOI

• Abstract PS1-09-14: Evaluating clinical and molecular correlates of Inflammatory Breast Cancer using a scoring system-based chart review

  Clinical Cancer Research · 2026-02-17

  article

  Abstract Background: Inflammatory breast cancer (IBC) is a rare and aggressive form of breast cancer with a distinct clinical presentation and poor prognosis. Diagnostic ambiguity remains a challenge, and recent literature has proposed structured criteria to improve case classification. Methods: We conducted a retrospective chart review of 83 patients diagnosed with IBC and 83 patients with non-inflammatory breast cancer (non-IBC), seen at the University of Texas Southwestern Medical Center as part of the Dallas Metastatic Cancer Study. Each IBC case was evaluated using a structured scoring system adapted from the diagnostic guidelines proposed by Omarini et al. (2022) to assess the degree of conformity to established IBC features. Clinical and pathological characteristics were compared across groups using appropriate statistical tests. Results: Our findings reinforce several established associations in the literature. Compared to non-IBC patients, those with IBC exhibited significantly higher Ki-67 proliferation indices (1.42-fold increase, p<0.0001, Mann-Whitney U test), greater number of metastatic sites (2-fold increase, p<0.0001, Mann-Whitney U test), and higher clinical stage at diagnosis (p = 0.04, Chi-square test). IBC cases were also associated with more aggressive disease biology as they were more likely to be ER negative (p = 0.003, Fisher test) and PR negative (p = 0.0184, Fisher test). Notably, we observed a novel pattern: IBC was significantly associated with specific metastatic sites, particularly the brain (4.5 times more likely in IBC patients, p<0.0001, Chi-square test) and lungs (2.08 times more likely in IBC, p = 0.0028, Chi-square test), suggesting a potentially distinct metastatic tropism. Conclusions: This study supports the diagnostic utility of a structured scoring system for IBC and confirms key clinical and molecular trends observed in prior research. The novel association with specific metastatic sites warrants further investigation and may inform future efforts in IBC classification and management. Citation Format: C. M. Atallah, A. Varner, C. J. Kang, P. Gowda, K. Anderson, D. Tovar, R. Morey, C. Hauer, R. Sridharan, S. Huang, K. Lei, S. M. Reddy, H. L. McArthur, J. Maués, C. Hodgdon, B. Zhang, X. Zhang, B. Lim, I. S. Chan. Evaluating clinical and molecular correlates of Inflammatory Breast Cancer using a scoring system-based chart review [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS1-09-14.

  PublisherDOI

• Abstract PS4-06-11: Initial Results from Correlative Analysis of a Single Arm Phase 2 Study of Peri-Operative Immune Checkpoint Inhibition and Cryoablation in Women with Hormone Receptor-Negative, HER2-Negative Early Stage/Resectable Breast Cancer

  Clinical Cancer Research · 2026-02-17

  article

  Abstract Background: Triple negative breast cancer (TNBC) is a biologically distinct subtype with a high risk of early relapse, particularly in patients with residual disease following neoadjuvant chemotherapy (NAC). Failure to achieve a complete response may reflect underlying immune evasion mechanisms, including upregulation of immune checkpoints such as programmed cell death protein 1 (PD-1), which impair effective T cell-mediated antitumor responses. Cryoablation (cryo) can stimulate T-cell priming and reduce MDSCs to overcome resistance to immune checkpoint inhibition (ICI). Preclinical and early clinical data suggest that the combination of cryo with ICI may synergistically improve immune activation. We conducted a multi-center, single arm, phase 2 study to evaluate the impact of cryo with standard-of-care pembrolizumab (pembro) in women with residual TNBC after taxane-based neoadjuvant chemotherapy (NAC), a group at high risk of early relapse (NCT03546686). Methods: Eligible women are ≥18y, with ER < 10%, PR < 10%, HER2 negative (per ASCO/CAP definition), ≥ 1.0 cm, residual operable disease after taxane-based NAC. Patients underwent percutaneous, image-guided cryo with concurrent research core biopsy 7-10 days prior to surgery and receive peri-operative pembro per standard-of-care. Peripheral blood was collected pre- and post-cryo, and flow cytometry was performed on paired peripheral blood mononuclear cells (PBMCs) from an initial cohort (n = 5) to identify changes in immune response. Results: Post-cryo, we observed an overall trend in the decrease of PD1-positive T cells and myeloid cells. PD1+CD8+ T cells decreased by 2.9-fold, PD1+CD4+ T cells decreased by 4.6-fold and PD1+CD3- decreased by 6.3-fold. Notably, we observed a decrease in CD11b+CD3- MDSCs by 14.92-fold. Additional exploratory correlative studies on tumor and blood, including tumor infiltrating lymphocytes and tumor PD-1 IHC, are ongoing to fully characterize the immunologic impact of the intervention and to explore predictors of efficacy. Conclusion: These initial results suggest that the addition of cryo to pembro may act synergistically to reduce the overall immunosuppressive immune environment, potentially resulting in improved immunity in patients with high-risk residual TNBC. Funding sources: Susan G. Komen, B-SEARCH, Conquer Cancer Foundation, Breast Cancer Research Foundation, Boston Scientific. Citation Format: S. Bhandari, A. Alhalwani, I. Terrazas, R. Sridharan, S. Rice, H. L. McArthur, I. S. Chan. Initial Results from Correlative Analysis of a Single Arm Phase 2 Study of Peri-Operative Immune Checkpoint Inhibition and Cryoablation in Women with Hormone Receptor-Negative, HER2-Negative Early Stage/Resectable Breast Cancer [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS4-06-11.

  PublisherDOI

• KDM3A and KDM3B regulate alternative splicing in mouse pluripotent stem cells

  iScience · 2025-05-08 · 1 citations

  articleOpen accessSenior author

  . Our findings reveal non-canonical roles of histone demethylating enzymes in splicing to regulate cell identity.

  PublisherDOI

• Uncovering Functional Gene Regulatory Networks in Bulk and Single-Cell Data through Robust Transcription Factor Activity Estimation and Model-Guided Experimental Validation

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-13 · 2 citations

  preprintOpen access

  Reconstructing genome-scale gene regulatory networks (GRNs) remains a difficult problem in systems biology, and many experimental and computational methods have been developed to address this problem. Recent computational methods have aimed to more accurately model GRNs by estimating the hidden Transcription Factor Activity (TFA) from prior knowledge of TF target regulatory connections, encoded as an input directed graph, to relax the assumption that mRNA level of the regulator correlates with the protein activity of the regulator. However, the noise in the prior knowledge can adversely affect the estimated TFA levels and the quality of the downstream inferred GRNs. Here, we present a new approach, MERLIN+P+TFA, that uses prior knowledge-guided sparsity regularization to robustly and accurately estimate TFA and downstream GRNs. We apply our method to simulated and real expression data in yeast and mammalian systems and show improved quality of inferred GRNs for both bulk and single-cell datasets. Regularized TFA offers benefits to a variety of other GRN inference algorithms, including those that have traditionally been used with expression alone, in both bulk and scRNA-seq settings. We used the inferred GRN to prioritize key regulators for the mouse Embryonic Stem Cell (mESC) state and validate 58 regulators experimentally. We identified both known and novel regulators of the mESC state and further validate the targets of 4 known and novel regulators. Our validation experiments suggest that computationally inferred networks can capture functional targets of TFs with higher precision than estimated in current benchmarks, however, it is important to generate context-specific gold standards.

  PublisherOA PDFDOI

• DOT1L induces RNAPII accumulation independent of its catalytic activity in pluripotent stem cells

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-09

  preprintOpen accessSenior authorCorresponding

  Abstract Pluripotent stem cells can be propagated in vitro from embryos in specific culture conditions that capture subtle developmental transitions. Naïve pluripotent mouse embryonic stem cells (ESCs) can exist in two distinct epigenetic states—the metastable state in serum/LIF conditions and the ground state with pharmacological inhibition of differentiation-inducing pathways in the 2i/LIF conditions, which better resembles the in vivo blastocyst. Here, we acutely induced one feature of 2i/LIF ESCs, an increase in the H3K79 methyltransferase, DOT1L, in serum/LIF ESCs to determine its effects on metastable pluripotency. We find that DOT1L induction causes an increase in RNA Polymerase II (RNAPII) accumulation at the transcription start site, irrespective of catalytic activity, mimicking 2i/LIF RNAPII pattern. However, the pulse of DOT1L and consequent RNAPII accumulation is insufficient to induce immediate changes in steady-state or nascent RNA expression. Genes with higher transcription and elongation rates exhibit moderate changes in RNAPII accumulation, while lowly transcribed genes separate into two distinct groups, with one group showing the strongest RNAPII accumulation in response to DOT1L induction and the other showing the weakest. This differential accumulation is reduced at H3K27me3-enriched and bivalent genes. We also find that cells that sustain DOT1L expression have a homogenous NANOG protein profile without affecting Nanog transcription. Taken together, we find that a pulse of DOT1L in serum/LIF ESCs is sufficient to partially recapitulate certain features of ground state pluripotency, reinforcing its importance in this state of the pluripotency continuum.

  PublisherOA PDFDOI

• KDM3A and KDM3B Maintain Naïve Pluripotency Through the Regulation of Alternative Splicing

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-06-01 · 1 citations

  preprintOpen accessSenior authorCorresponding

  ABSTRACT Histone modifying enzymes play a central role in maintaining cell identity by establishing a conducive chromatin environment for lineage specific transcription factor activity. Pluripotent embryonic stem cell (ESC) identity is characterized by a lower abundance of gene repression associated histone modifications that enables rapid response to differentiation cues. The KDM3 family of histone demethylases removes the repressive histone H3 lysine 9 dimethylation (H3K9me2). Here we uncover a surprising role for the KDM3 proteins in the maintenance of the pluripotent state through post-transcriptional regulation. We find that KDM3A and KDM3B interact with RNA processing factors such as EFTUD2 and PRMT5. Acute selective degradation of the endogenous KDM3A and KDM3B proteins resulted in altered splicing independent of H3K9me2 status or catalytic activity. These splicing changes partially resemble the splicing pattern of the more blastocyst-like ground state of pluripotency and occurred in important chromatin and transcription factors such as Dnmt3b, Tbx3 and Tcf12 . Our findings reveal non-canonical roles of histone demethylating enzymes in splicing to regulate cell identity.

  PublisherOA PDFDOI

• Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets

  Zenodo (CERN European Organization for Nuclear Research) · 2023-04-17

  datasetOpen access

  The uploaded files are source datasets for the scMTNI algorithm. scMTNI is a multi-task learning framework that integrates the cell lineage structure, scRNA-seq and scATAC-seq measurements to enable joint inference of cell type-specific GRNs. See more details at Zhang, S., Pyne, S., Pietrzak, S. et al. Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets. Nat Commun 14, 3064 (2023). https://doi.org/10.1038/s41467-023-38637-9 The source data scMTNI_sourcedata.tar.gz contains the following 3 parts: 1) The cluster-specific scRNA-seq matrices and the prior networks for all three datasets and scMTNI inferred consensus networks. 2) Gold standard human and mouse datasets for evaluation. 3) Source data for scMTNI figures 2-8 and supplementary figures. The key for each figure and its corresponding file path is in SourceData_Key_v2.xlsx. The source data Buenrostro_Hematopoiesis.tar.gz contains the scRNA-seq data for human hematopoietic differentiation downloaded from Data S2 of Buenrostro et al. The source data RawMotifFiles.tar.gz contains the motif instance files and promoter files for human and mouse for generating prior networks using scATAC-seq data for scMTNI. Check https://github.com/Roy-lab/scMTNI/blob/master/Scripts/genPriorNetwork/readme.md for examples and scripts.

  PublisherDOI

• DOT1L interaction partner AF10 controls patterning of H3K79 methylation and RNA polymerase II to maintain cell identity

  Stem Cell Reports · 2023-11-22 · 5 citations

  articleOpen accessSenior authorCorresponding

  Histone 3 lysine 79 methylation (H3K79me) is enriched on gene bodies proportional to gene expression levels and serves as a strong barrier for the reprogramming of somatic cells to induced pluripotent stem cells (iPSCs). DOT1L is the sole histone methyltransferase that deposits all three orders-mono (me1), di (me2), and tri (me3) methylation-at H3K79. Here, we leverage genetic and chemical approaches to parse the specific functions of orders of H3K79me in maintaining cell identity. DOT1L interacts with AF10 (Mllt10), which recognizes unmodified H3K27 and boosts H3K79me2/3 methylation. AF10 deletion evicts H3K79me2/3 and reorganizes H3K79me1 to the transcription start site to facilitate iPSC formation in the absence of steady-state transcriptional changes. Instead, AF10 loss redistributes RNA polymerase II to a uniquely pluripotent pattern at highly expressed, rapidly transcribed housekeeping genes. Taken together, we reveal a specific mechanism for H3K79me2/3 located at the gene body in reinforcing cell identity.

  PublisherOA PDFDOI

• Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets

  Zenodo (CERN European Organization for Nuclear Research) · 2023-04-17 · 1 citations

  datasetOpen access

  The uploaded files are source datasets for the scMTNI algorithm. scMTNI is a multi-task learning framework that integrates the cell lineage structure, scRNA-seq and scATAC-seq measurements to enable joint inference of cell type-specific GRNs. See more details at Preprint: https://biorxiv.org/cgi/content/short/2022.07.25.501350v1. The source data scMTNI_sourcedata.tar.gz contain the following 3 parts: 1) The cluster-specific scRNA-seq matrices and the prior networks for all three datasets and scMTNI inferred consensus networks. 2) Gold standard human and mouse datasets for evaluation. 3) Source data for scMTNI figures 2-8 and supplementary figures. The key for each figure and its corresponding file path is in SourceData_Key_v2.xlsx. The source data Buenrostro_Hematopoiesis.tar.gz contains the scRNA-seq data for human hematopoietic differentiation downloaded from Data S2 of Buenrostro et al.

  PublisherDOI

Recent grants

• Collaboration of chromatin remodeling and signaling pathways in pluripotency

  NIH · $2.9M · 2015–2024

Frequent coauthors

• Sushmita Roy

  University of Wisconsin–Madison

  47 shared

• Alireza Fotuhi Siahpirani

  University of Tehran

  40 shared

• Kathrin Plath

  39 shared

• Stefan Pietrzak

  Wisconsin Institutes for Discovery

  31 shared

• Coral K. Wille

  Wisconsin Institutes for Discovery

  31 shared

• Sunnie Grace McCalla

  University of Wisconsin–Madison

  30 shared

• Shilu Zhang

  University of Science and Technology of China

  22 shared

• Spencer Halberg

  22 shared

Labs

• Sridharan LabPI